Download the Baran-Gale, et al. ageing thymus data
download_thymus_ageing.RdDownloads the mouse ageing thymus droplet experiment as a
SingleCellExperiment. Roughly 69k thymic epithelial cells across three
ages, with real change in cell type proportions between them.
That compositional change is what makes it the example for
get_miloR_abundances_sc() and meld_sc(). A
stimulation experiment moves cells in embedding space without moving the
proportions, so almost every neighbourhood comes out significant and the
result says nothing. Load it with load_sce().
Details
Sourced from the MouseThymusAgeing Bioconductor package. See
data-raw/zenodo_sce_datasets.R for the preparation. The object carries no
gene names, so load_sce() falls back to the Ensembl identifiers
in the rowData, and 336 genes with no annotation at all get a generated
identifier.
Served from the bixverse-data GitHub release. There is no Zenodo fallback
for this one yet. At 430 MB it is the largest of the example datasets, so
expect the first call to take a while.
Examples
if (FALSE) { # \dontrun{
# pulls the archive into the session tempdir()
path <- download_thymus_ageing()
sce <- qs2::qs_read(path)
} # }